There are alot of ways to get the tunnels to work, I just used the 'set to height' tool under the terrain. Set the entire 'ground level' to 100 and they 'carved' out tunnels using the 'square' brush at 100 hardness along the path of the tunnels at a 'height' of 95, then placed Side walks over the top of the tunnels. I also had to copy the sidewalks and turn them 'up-side-down' so you couldn't see through them while inside. I used a few other things to 'pretty' them up, large logs for support beams, textures to appear like a 'floor' and a few posters/signs on the walls.
FYI, if you downloaded my map, you should delete it and go download it again...I am up to 'Fort Oasis v4' right now. If you just search for 'AoR' under creator it will come right up.